Setting up a lathe for CNC and was wondering if ball screw pitch can be different between the Z axis (5MM) and X axis (4MM). Had to get a smaller ball screw for my X to physically make it fit and found out it was 4MM pitch.

Yes, Mach 3 will let you set up each axis with different leads or different motors. It is calculated in the turns per inch entry if your are using imperial setups. If you are setting up a metric setup it wants distance of travel per one turn of the motor.

So a .200" lead would be 5 tuns per inch and so on. You can use metric ball screws and still set up your machine as "inches" but you'll have to do some extra math.

I'd second that, even though I am still running a Mach 3 lathe conversion. Centroid is Funac compatible and runs a full set of G-codes while Mach 3 runs a partial set and is not compatible with anything else, as far as I'm aware. You will need a spindle encoder, a real one and not just the indexing type like mach uses, if you want to thread or do rigid tapping with the Acron/Centroid setup.

I'm in the process of reading the entire manual right now for the Centroid lathe and mill software. It is written very well, more like the way I understand tech manuals.

Ok, My poor explanation! Mach 3 uses a single slot spindle index and nothing else. So basically you make a disc with one slot in it, use an optical reader to read the slot or you can use one of those other type single pulse per rev encoders like a photo tac.

Mach 3 can't read a real 2000 line encoder for spindle positioning. Mach 3 also can't use CSS and FPR at the same time. (constant surface speed and Feed per Rev) One or the other but not both!